bijux-proteomics-runtime 0.3.8__py3-none-any.whl

LICENSE

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+      Copyright 2026 Bijan Mousavi <bijan@bijux.io>
+
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NOTICE

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+Copyright 2026 Bijan Mousavi <bijan@bijux.io>
+
+This repository is licensed under the Apache License, Version 2.0.

bijux_proteomics_runtime/__init__.py

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+"""Canonical runtime package for bijux proteomics execution surfaces."""
+
+from __future__ import annotations
+
+from importlib import import_module
+from typing import Any
+
+__all__ = ["AppConfig", "RunManager", "cli", "create_app"]
+
+_RUNTIME_ROOT_EXPORTS = {
+    "AppConfig": ("bijux_proteomics_runtime.api", "AppConfig"),
+    "RunManager": ("bijux_proteomics_runtime.runs.manager", "RunManager"),
+    "cli": ("bijux_proteomics_runtime.api.cli", "cli"),
+    "create_app": ("bijux_proteomics_runtime.api", "create_app"),
+}
+
+
+def __getattr__(name: str) -> Any:
+    """Load public runtime entrypoints lazily to avoid package-import cycles."""
+
+    target = _RUNTIME_ROOT_EXPORTS.get(name)
+    if target is None:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    module_name, attribute_name = target
+    module = import_module(module_name)
+    return getattr(module, attribute_name)

bijux_proteomics_runtime/api/__init__.py

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+# SPDX-License-Identifier: Apache-2.0
+# Copyright © 2025 Bijan Mousavi
+
+"""HTTP API entry points."""
+
+from __future__ import annotations
+
+from bijux_proteomics_runtime.api.public import (
+    __all__ as __all__,
+)
+from bijux_proteomics_runtime.api.public import (
+    __getattr__ as __getattr__,
+)
+
+__stability__ = "stable"

bijux_proteomics_runtime/api/app.py

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+# SPDX-License-Identifier: Apache-2.0
+# Copyright © 2025 Bijan Mousavi
+
+"""FastAPI app factory."""
+
+from __future__ import annotations
+
+from collections.abc import Awaitable, Callable, Iterable
+from dataclasses import dataclass
+from pathlib import Path
+from re import Pattern
+
+from fastapi import FastAPI, HTTPException, Request, Response, status
+from fastapi.exceptions import RequestValidationError
+from fastapi.responses import JSONResponse
+from starlette.exceptions import HTTPException as StarletteHTTPException
+from starlette.routing import Match
+
+from bijux_proteomics_runtime.api.errors import (
+    ApiError,
+    http_error,
+    method_not_allowed,
+    ok_envelope,
+    validation_error,
+)
+from bijux_proteomics_runtime.api.request_logging import (
+    RequestIdMiddleware,
+    RequestLogMiddleware,
+)
+from bijux_proteomics_runtime.api.v1.router import router as v1_router
+from bijux_proteomics_runtime.api.v1.schema import ApiEnvelope
+from bijux_proteomics_runtime.providers.catalog import (
+    provider_metadata,
+    provider_requirements,
+)
+from bijux_proteomics_runtime.runs.correlation import (
+    build_request_correlation_meta,
+)
+from bijux_proteomics_runtime.support.identity import (
+    runtime_banner,
+    runtime_description,
+    runtime_title,
+)
+
+
+def _iter_method_guard_routes(app: FastAPI) -> Iterable[tuple[Pattern[str], set[str]]]:
+    """Yield concrete HTTP route matchers for the custom method guard."""
+
+    for route in app.router.routes:
+        route_methods = _route_methods_for_guard(getattr(route, "methods", None))
+        path_regex = getattr(route, "path_regex", None)
+        if route_methods and path_regex is not None:
+            yield path_regex, route_methods
+            continue
+        effective_route_contexts = getattr(route, "effective_route_contexts", None)
+        if not callable(effective_route_contexts):
+            continue
+        for context in effective_route_contexts():
+            context_methods = _route_methods_for_guard(
+                getattr(context, "methods", None)
+            )
+            context_path_regex = getattr(context, "path_regex", None)
+            if context_methods and context_path_regex is not None:
+                yield context_path_regex, context_methods
+
+
+def _route_methods_for_guard(candidate: object) -> set[str]:
+    """Return a method set only when a route exposes concrete string methods."""
+
+    if not isinstance(candidate, (set, frozenset)):
+        return set()
+    if not all(isinstance(method, str) for method in candidate):
+        return set()
+    return set(candidate)
+
+
+@dataclass(frozen=True)
+class AppConfig:
+    """AppConfig."""
+
+    base_dir: Path
+    docs_enabled: bool = True
+    title: str = runtime_title()
+    description: str = runtime_description()
+    version: str = "2.0.0"
+
+
+def create_app(config: AppConfig) -> FastAPI:
+    """Create a configured FastAPI app.
+
+    Inputs:
+    ``config`` must provide the runtime base directory plus the app title,
+    description, version, and documentation toggle policy.
+
+    Outputs:
+    Returns one configured ``FastAPI`` application with runtime middleware,
+    exception handlers, provider metadata routes, and versioned API routers.
+
+    Failure Modes:
+    Propagates FastAPI router registration, middleware construction, and route
+    handler setup failures during application assembly.
+
+    Scientific Caveats:
+    This factory assembles transport and operator wiring only; it does not
+    validate scientific inputs or execute workflow algorithms at creation time.
+    """
+    docs_url = "/docs" if config.docs_enabled else None
+    redoc_url = "/redoc" if config.docs_enabled else None
+    openapi_url = "/openapi.json" if config.docs_enabled else None
+
+    app = FastAPI(
+        title=config.title,
+        description=config.description,
+        version=config.version,
+        docs_url=docs_url,
+        redoc_url=redoc_url,
+        openapi_url=openapi_url,
+    )
+    app.state.base_dir = config.base_dir
+
+    app.add_middleware(RequestIdMiddleware)
+    app.add_middleware(RequestLogMiddleware)
+
+    @app.middleware("http")
+    async def _method_guard(
+        request: Request, call_next: Callable[[Request], Awaitable[Response]]
+    ) -> Response:
+        """Return 405 for unsupported methods on known routes."""
+        scope = request.scope
+        if scope.get("type") == "http":
+            request_path = scope.get("path")
+            matched = False
+            allowed_methods: set[str] = set()
+            if isinstance(request_path, str):
+                for path_regex, route_methods in _iter_method_guard_routes(app):
+                    if path_regex.match(request_path) is not None:
+                        matched = True
+                        allowed_methods.update(route_methods)
+            else:
+                for route in app.router.routes:
+                    match, _ = route.matches(scope)
+                    if match in {Match.FULL, Match.PARTIAL}:
+                        matched = True
+                        route_methods = _route_methods_for_guard(
+                            getattr(route, "methods", None)
+                        )
+                        if route_methods:
+                            allowed_methods.update(route_methods)
+            if matched and request.method not in allowed_methods:
+                allow_header = ", ".join(sorted(allowed_methods))
+                meta = build_request_correlation_meta(
+                    request,
+                    "method-guard",
+                    request.url.path,
+                )
+                payload = method_not_allowed(
+                    f"Method {request.method} not allowed.",
+                    str(request.url),
+                    meta=meta,
+                )
+                return JSONResponse(
+                    status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
+                    content=payload,
+                    headers={"Allow": allow_header},
+                )
+        return await call_next(request)
+
+    @app.exception_handler(ApiError)
+    async def _handle_api_error(request: Request, exc: ApiError) -> JSONResponse:
+        """_handle_api_error."""
+        return JSONResponse(status_code=exc.status_code, content=exc.payload)
+
+    @app.exception_handler(HTTPException)
+    async def _handle_http_exception(
+        request: Request, exc: HTTPException
+    ) -> JSONResponse:
+        """_handle_http_exception."""
+        payload = http_error(
+            exc.status_code,
+            str(exc.detail),
+            str(request.url),
+            meta=build_request_correlation_meta(
+                request, "http-error", request.url.path
+            ),
+        )
+        return JSONResponse(status_code=exc.status_code, content=payload)
+
+    @app.exception_handler(StarletteHTTPException)
+    async def _handle_starlette_http_exception(
+        request: Request, exc: StarletteHTTPException
+    ) -> JSONResponse:
+        """_handle_starlette_http_exception."""
+        payload = http_error(
+            exc.status_code,
+            str(exc.detail),
+            str(request.url),
+            meta=build_request_correlation_meta(
+                request,
+                "starlette-http-error",
+                request.url.path,
+            ),
+        )
+        return JSONResponse(status_code=exc.status_code, content=payload)
+
+    @app.exception_handler(RequestValidationError)
+    async def _handle_validation_error(
+        request: Request, exc: RequestValidationError
+    ) -> JSONResponse:
+        """_handle_validation_error."""
+        payload = validation_error(
+            str(exc),
+            str(request.url),
+            meta=build_request_correlation_meta(
+                request,
+                "validation-error",
+                request.url.path,
+            ),
+        )
+        return JSONResponse(
+            status_code=status.HTTP_422_UNPROCESSABLE_CONTENT, content=payload
+        )
+
+    @app.get("/health", tags=["health"], response_model=ApiEnvelope)
+    @app.get("/api/v1/health", tags=["health"], response_model=ApiEnvelope)
+    def health(request: Request) -> dict[str, object]:
+        """health."""
+        return ok_envelope(
+            {"status": "ok", "runtime": runtime_banner()},
+            meta=build_request_correlation_meta(request, "health", "/health"),
+        )
+
+    @app.get("/ready", tags=["health"], response_model=ApiEnvelope)
+    @app.get("/api/v1/ready", tags=["health"], response_model=ApiEnvelope)
+    def ready(request: Request) -> dict[str, object]:
+        """ready."""
+        providers: dict[str, object] = {}
+        try:
+            for name in provider_metadata():
+                providers[name] = {
+                    "requirements": provider_requirements(name),
+                }
+            status_value = "ok"
+        except Exception as exc:  # noqa: BLE001
+            providers = {"error": [str(exc)]}
+            status_value = "degraded"
+        return ok_envelope(
+            {
+                "status": status_value,
+                "runtime": runtime_banner(),
+                "providers": providers,
+            },
+            meta=build_request_correlation_meta(request, "ready", "/ready"),
+        )
+
+    app.include_router(v1_router, prefix="/api/v1")
+    return app
+
+
+app = create_app(AppConfig(base_dir=Path.cwd(), docs_enabled=True))